5KH7

Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J.Walker, J.Ravichandran, M.Ferreira de Freitas, R.Schapira, M.Bountra, C.Edwards, A.M.Santhakumar, V.Arrowsmith, C.M.Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 6
A
107Homo sapiensGene Names: HDAC6 (KIAA0901)
EC: 3.5.1.98
Find proteins for Q9UBN7 (Homo sapiens)
Go to Gene View: HDAC6
Go to UniProtKB:  Q9UBN7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
6T7
Query on 6T7

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Download CCD File 
A
3-(6-oxidanylidene-3-pyridin-3-yl-pyridazin-1-yl)propanoic acid
C12 H11 N3 O3
FPHNPEYKDLCEEE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 40.719α = 90.00
b = 43.776β = 90.00
c = 55.924γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release